A5083231687- Lipid Membrane Structure and Behavior
- Dendrimers and Hyperbranched Polymers
- Surfactants and Colloidal Systems
- Cellular transport and secretion
- RNA Interference and Gene Delivery
- Spectroscopy and Quantum Chemical Studies
- Bacteriophages and microbial interactions
- Antimicrobial Peptides and Activities
- Protein Structure and Dynamics
- Photodynamic Therapy Research Studies
- Force Microscopy Techniques and Applications
- Advanced biosensing and bioanalysis techniques
- Protein purification and stability
- Quantum Dots Synthesis And Properties
- Crystallization and Solubility Studies
- Electrostatics and Colloid Interactions
- Drug Solubulity and Delivery Systems
- Advanced Polymer Synthesis and Characterization
- Chalcogenide Semiconductor Thin Films
- Protein Interaction Studies and Fluorescence Analysis
- Nanowire Synthesis and Applications
- RNA and protein synthesis mechanisms
- Erythrocyte Function and Pathophysiology
- Nanoplatforms for cancer theranostics
- Block Copolymer Self-Assembly
Indian Institute of Technology Kanpur
2021-2025
Boston University
2019-2022
Indian Institute of Science Bangalore
2012-2020
University of Michigan
2016-2018
Ann Arbor Center for Independent Living
2018
BioSurfaces (United States)
2016-2018
Michigan United
2016
Abstract Confronted with the rapid evolution and dissemination of antibiotic resistance, there is an urgent need to develop alternative treatment strategies for drug‐resistant pathogens. Here, unconventional approach presented restore susceptibility methicillin‐resistant S. aureus (MRSA) a broad spectrum conventional antibiotics via photo‐disassembly functional membrane microdomains. The microdomains based on effective photolysis staphyloxanthin, golden carotenoid pigment that gives its...
To investigate the ability of coarse-grained molecular dynamics simulations to predict relative growth rates crystal facets pharmaceutical molecules, we apply two coarse-graining strategies drug phenytoin and carbamazepine. In first method, map an atomistic model a MARTINI-level (CG) force field that uses 2 or 3 heavy atoms per bead. This is followed by applying Particle Swarm Optimization (PSO), global optimum searching algorithm, CG Lennard-Jones intermolecular potentials fit radial...
Bare faceted gold nanoparticles (AuNPs) have a tendency to aggregate through preferred attachment of the [111] surfaces. We used fully atomistic classical molecular dynamics simulations obtain quantitative estimate this surface interaction using umbrella sampling (US) at various temperatures. To tune interaction, we use polyamidoamine (PAMAM) dendrimer coat under conditions. observe spontaneous adsorption protonated as well nonprotonated PAMAM on AuNP surface. The adsorbed nanoparticle...
One of the major challenges nanomedicine and gene therapy is effective translocation drugs genes across cell membranes. In this study, we describe a systematic procedure that could be useful for efficient drug delivery into cell. Using fully atomistic molecular dynamics (MD) simulations, show molecules various shapes, sizes, chemistries can spontaneously encapsulated in single-walled carbon nanotube (SWCNT) embedded 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, as...
Deterministic formation of membrane scission necks by protein machinery with multiplexed functions is critical in biology. A microbial example M2 viroporin, a proton pump from the influenza virus that remodeling activity to induce budding and host during viral maturation. In comparison, dynamin family constitutes class eukaryotic proteins implicated mitochondrial fission, as well various endocytosis pathways. case Dnm1, fission yeast, mechanoenzyme create necks. It not clear why these are...
The MARTINI force field is one of the most used coarse-grained models for biomolecular simulations. Many limitations model including protein-protein overaggregation have been improved in its latest version, MARTINI-3. In this study, we investigate efficacy MARTINI-3 parameters capturing interactions peripheral proteins with plasma membranes. Particularly, consider two classes proteins, namely, annexin and epsin, which are known to generate negative positive membrane curvatures, respectively....
We present a method of modeling nanoparticle (NP) hydrophobicity using coarse-grained molecular dynamics (CG MD) simulations, and apply this to the interaction lipids with nanoparticles. To model at level wettability or given material, we choose MARTINI force field, determine through simulation contact angles water droplets residing on flat regular surfaces composed various bead types (C1, C2, etc.). Each surface is single type in each three crystallographic symmetries (FCC, BCC, HCP). While...
Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed several virulent bacterial strains, on a target cell is challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as pH controlled gating devices once the has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize cytolysin A (ClyA) protein modified with fifth generation (G5) dendrimers. Our results show...
We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function atomistic simulations known crystal. With we show that CG drug phenytoin growth crystalline slab melt phenytoin, allowing determination fastest-growing surface, as well giving correct lattice parameters crystal morphology. By applying...
Peptide-induced transmembrane pore formation is commonplace in biology. Examples of pores include formed by antimicrobial peptides (AMPs) and cell-penetrating (CPPs) bacterial membranes eukaryotic membranes, respectively. In general, however, depends on peptide sequences, lipid compositions, intensive thermodynamic variables difficult to observe directly under realistic solution conditions, with structures that are challenging measure directly. contrast, the structure phase behavior...
We present coarse-grained (CG) force fields for hydroxypropyl-methylcellulose acetate succinate (HPMCAS) polymers and the drug molecule phenytoin using a bead/stiff spring model, with each bead representing HPMCAS monomer or side group (hydroxypropyl acetyl, succinyl) single ring. obtain bonded nonbonded interaction parameters in our CG model RDFs from atomistic simulations of short oligomers (20-mer) molecules. The interactions are modeled LJ 12-6 potential, separate substitution type,...
Using fully atomistic simulations, we find that the structure of critical urea crystal nucleus (monoclinic, four molecules per unit cell) in an aqueous solution differs from known bulk (orthorhombic, two cell). Following a frequently used "seeding technique" combined with classical nucleation theory, also at room temperature is very large (containing ∼530 molecules) and rate slow (∼5×10-24cm-3s-1), suggesting homogeneous improbable temperature.
The mechanisms by which peripheral membrane proteins generate curvature is currently an active area of research. One the proposed amphipathic insertion or 'wedge' mechanism in protein shallowly inserts helix inside to drive curvature. However, recent experimental studies have challenged efficiency as it requires unusual densities. These alternative mechanism, namely 'protein-crowding', lateral pressure generated random collisions among bound drives bending. In this study, we employ atomistic...
We present a multi-scale simulation method for modeling crystal growth in the presence of polymer excipients. The includes coarse-grained (CG) model small molecules known structure whose force field is obtained using structural properties from atomistic simulations. This CG capable stabilizing molecular and capturing melt wide range organic molecules, as demonstrated by application our to isoniazid, urea, sulfamethoxazole, prilocaine, oxcarbazepine, phenytoin. can also be used study effect...
Using coarse-grained molecular dynamics simulations and an umbrella sampling method that uses local surfactant density as a reaction coordinate, we directly calculate, for the first time, both scission branching free energies of model charged micelle [cationic cetyltrimethylammonium chloride (CTAC)] in presence inorganic organic salts (hydrotropes). We find while salt only weakly affects energy, hydrotropes produce strong, nonmonotonic dependence energy on concentration. The nonmonotonicity...
Using all-atom molecular dynamics simulation, we have studied the effect of size and temperature on strain induced phase transition wurtzite CdSe nanowires. The structure transforms into a five-fold coordinated under uniaxial along c axis. Our results show that lower smaller nanowires stabilize which is not stable in bulk CdSe. High reversibility this transformation with very small heat loss will make these suitable for building efficient nanodevices.
We have performed fully atomistic classical molecular dynamics simulations to calculate the effective interaction between two polyamidoamine dendrimers. Using umbrella sampling technique, we obtained potential of mean force (PMF) dendrimers and investigated effects protonation level dendrimer size on PMF. Our results show that can be tuned from purely repulsive partly attractive by changing level. The PMF profiles are well-fitted sum an exponential a Gaussian function with weight dominating...
Mechanical properties of ZnS nanowires and thin films are studied as a function size growth direction using all-atom molecular dynamics simulations. Using the stress-strain relationship we extract Young's moduli at room temperature. Our results show that modulus [0001] has strong dependence. On other hand, $[01\overline{1}0]$ do not exhibit dependence in range have investigated. We provide microscopic understanding this behavior on basis bond stretching contraction due to rearrangement atoms...